Crystal structure of aspartyl-tRNA synthetase from Pyrococcus kodakaraensis KOD: archaeon specificity and catalytic mechanism of adenylate formation

The EMBO Journal
E SchmittDino Moras


The crystal structure of aspartyl-tRNA synthetase (AspRS) from Pyrococcus kodakaraensis was solved at 1.9 A resolution. The sequence and three-dimensional structure of the catalytic domain are highly homologous to those of eukaryotic AspRSs. In contrast, the N-terminal domain, whose function is to bind the tRNA anticodon, is more similar to that of eubacterial enzymes. Its structure explains the unique property of archaeal AspRSs of accommodating both tRNAAsp and tRNAAsn. Soaking the apo-enzyme crystals with ATP and aspartic acid both separately and together allows the adenylate formation to be followed. Due to the asymmetry of the dimeric enzyme in the crystalline state, different steps of the reaction could be visualized within the same crystal. Four different states of the aspartic acid activation reaction could thus be characterized, revealing the functional correlation of the observed conformational changes. The binding of the amino acid substrate induces movement of two invariant loops which secure the position of the peptidyl moiety for adenylate formation. An unambiguous spatial and functional assignment of three magnesium ion cofactors can be made. This study shows the important role of residues present in both archaea...Continue Reading


Mar 1, 1991·Acta Crystallographica. Section A, Foundations of Crystallography·T A JonesM Kjeldgaard
Nov 1, 1989·Proceedings of the National Academy of Sciences of the United States of America·P H HirelS Blanquet
Oct 1, 1993·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·M Delarue, D Moras
Aug 15, 1996·Nature·A W CurnowD Söll
Aug 20, 1996·Proceedings of the National Academy of Sciences of the United States of America·W F Doolittle
Jun 1, 1997·Trends in Biochemical Sciences·J G Arnez, D Moras
Jul 8, 1997·Proceedings of the National Academy of Sciences of the United States of America·J G ArnezC S Francklyn
Jun 27, 1997·Cell·G J Olsen, C R Woese
Jun 27, 1997·Cell·P P Dennis
Mar 21, 1998·Journal of Molecular Biology·G ArchontisM Karplus

❮ Previous
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